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14.P: Problems for Chapter 14

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P14.1:  Enolase catalyzes the reaction shown below.  An active site lysine is thought to participate as a catalytic base, and a glutamic acid residue is though to participate as a catalytic acid.  The enzyme requires magnesium ion to function.  Propose a mechanism, showing the predicted roles of the Lys, Glu, and magnesium.

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P14.2: In one of its degradation pathways, threonine is first converted to alpha-ketobutyrate through an enamine intermediate.  Show a complete mechanism for this reaction.

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P14.3: The amino acid aspartate undergoes elimination of ammonia as part of its degradation pathway.  Show the expected result of this elimination.

P14.4:  N-ethylmaleimide is an irreversible inactivator of many enzymes that contain active site cysteines.  Show how this inactivation could occur, and show the structure of the labeled cysteine.

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P14.5:

a) Provide a likely mechanism for the following reaction from the biosynthesis of the amino acid valine:

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b) In a newly discovered pathway for the biosynthesis (in bacteria) of the building block compound for isoprenoid biosynthesis, pyruvate and glyceraldehyde-3-phosphate condense, with the release of carbon dioxide.  The reaction requires a coenzyme.  Draw a complete mechanism for this reaction, showing the product formed and the role of the coenzyme.

P14.6: Show the product and provide a mechanism for the following Michael addition reaction.

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P14.7: The following substrate undergoes an E1cb dehydration followed by re-hydration to form a different constitutional isomer.  Predict the structure of the isomer, and also the structure of the intermediate structure.

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P14.8:  Both reactions below are thought to involve elimination by the E1 mechanism.

a) Predict the product, and propose a mechanism:

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b) Propose a mechanism:

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P14.9: Predict the second product for this reaction.  What type of mechanism is it?

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P14.10:  All of the following reactions are PLP-dependent.   Draw mechanisms, showing the ‘electron sink’ action of PLP.  In each case, begin the substrate-PLP adduct, and end with the product-PLP adduct (in other words, you do not need to show the Schiff base being formed and later hydrolyzed)

a)  threonine  →  glycine + acetaldehyde  (IUPAC name ethanal)

b)

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c)

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P14.11: Propose a mechanism for this laboratory reaction:

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P14.12: The following reaction requires thiamine diphosphate as a cofactor.  Propose a mechanism that takes into account the role of TPP as an electron sink.

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P14.13: Draw all possible elimination products for the following starting materials:

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P14.14: Draw the transition state for an E2 reaction in which 2-bromobutane is converted to (E)-2-butene. Be sure to accurately show the geometry of the breaking bonds.

P14.15: The compounds below will not react by the E2 mechanism.  Explain why not.

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P14.16: Predict the most abundant product of each of the following (nonenzymatic) reactions, and state the mechanism by which the product forms.

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P14.17:  Draw a complete mechanism for the Robinson annulation reaction discussed in section 14.1D.

P14.18:  Predict the products of the following Robinson annulation reactions:

a)

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b)

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P14.19: Show the starting materials that you could use to synthesize the following compounds by Robinson annulation:

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P14.20: Predict the product of these laboratory reactions:

a)

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b)

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c)

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Challenge problems

C14.1: The reaction shown below, catalyzed by orotidine monophosphate decarboxylase, is one of the most extensively studied enzymatic transformations.  It is known to occur without the participation of any coenzymes.

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a) Look at  the reaction closely: what is unique about it?

b) In 1997, a paper was published in which the authors predicted, based on theoretical calculations, that this reaction proceeded through a carbene intermediate (carbenes are not covered in this text – you may need to look them up). This was  prior to the publication of an x-ray crystal structure.  What kind of active site environment does this imply?

c) When the crystal structure was published a few years later, we learned that an aspartate residue (predicted to be negatively charged) is positioned very near the substrate carboxylate group, and a lysine residue (predicted to be positively charged) is positioned nearby on the opposite side (see figure below).  What roles do you think were predicted for these two active site residues? 

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C14.2: 5,10-methylene tetrahydrofolate is a coenzyme that, like S-adenosylmethionine (SAM), serves to transfer single carbons.  Show a likely mechanism for the transformation shown below.

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C14.3: Suggest a mechanism for the following reaction:

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C14.4:

a) Given the transformation shown below (and no other information), predict a likely mechanism based on similar transformations we have seen previously.

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b) As is turns out, this reaction requires ATP and aspartate, and releases ADP, Pi, and fumarate.  Given this information, predict a different mechanism.

 

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C14.5: In the histidine degradation pathway, histidine undergoes elimination of ammonia to form trans-urocanate in what, at first glance, appears to be an E1-like mechanism similar to the dehydration reaction from histidine biosynthesis, detailed in section 14.3B. However, the enzyme catalyzing this reaction has been shown to use an unusual 'coenzyme', 4-methylideneimidazole-5-one (MIO), which is formed from the cyclization of an alanine-serine-glycine stretch of the enzyme itself. A mechanism has been proposed in which the MIO coenzyme plays the role of electron sink, and the intermediate shown below forms.

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Propose a full mechanism for this reaction according to this information.

 

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